|1740 Batavia massacre
|Massacre of Bau miners
||Bau (then part of Indonesia)
||December 9, 1947
||Balongsari, West Java
||Indonesians of Rawegede
||December 1946-February 1947
|Indonesian killings of 1965–1966
||October 1965-March 1966
||Jakarta, East Java, Bali
||Transition to the New Order
||Banyuwangi, East Java
||A witchhunt in Banyuwangi against alleged sorcerers spiraled into widepsread riots and violence. In addition to alleged sorcerers, Islamic clerics were also targeted and killed, Nahdlatul Ulama members were murdered by rioters.
|May 1998 riots of Indonesia
||4–8 and 12–15 May 1998
||Major riots occurred in Medan, Jakarta, and Surakarta with a number of isolated incidents elsewhere
||There were dozens of documented accounts of ethnic Chinese women being raped. Other sources note over 1,500 people were killed and over 468 (168 victims in Jakarta alone) were mass gang-raped in the riots. There is a possibility of 5000 dead. However, most of the people who died in the riots were the Javanese Indonesian looters who targeted the Chinese shops, not the Chinese themselves, since the looters were burnt to death in a massive fire.
||6 July 1998
||Biak Numfor Regency, Papua Province
||Indonesian military attack public gathering, conduct executions, dump bodies at sea.
||Sambas Regency, West Kalimantan
||In the Sambas riots in 1999 Muslim Malays and Animist Dayaks joined together to massacre the Muslim Madurese during the Sambas conflict. Madurese were mutilated, raped, and killed by the Malays and Dayaks and 3,000 of them died in the massacres, with the Indonesian government doing little to stop the violence.
||February 18, 2001
||Sampit, Central Kalimantan
||Dayak people massacred Madurese migrants